skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


Title: The Nopp140 gene in Drosophila melanogaster displays length polymorphisms in its large repetitive second exon
Nopp140, often called the nucleolar and Cajal body phosphoprotein (NOLC1), is an evolutionarily conserved chaperone for the transcription and processing of rRNA during ribosome subunit assembly. Metazoan Nopp140 contains an amino terminal LisH dimerization domain and a highly conserved carboxyl domain. A large central domain consists of alternating basic and acidic motifs of low sequence complexity. Orthologous versions of Nopp140 contain variable numbers of repeating basic–acidic units. While vertebrate Nopp140 genes use multiple exons to encode the central domain, the Nopp140 gene in Drosophila uses exclusively exon 2 to encode the central domain. Here, we define three overlapping repeat sequence patterns (P, P′, and P″) within the central domain of D. melanogaster Nopp140. These repeat patterns are poorly conserved in other Drosophila species. We also describe a length polymorphism in exon 2 that pertains specifically to the P′ pattern in D. melanogaster. The pattern displays either two or three 96 base pair repeats, respectively, referred to as Nopp140-Short and Nopp140-Long. Fly lines homozygous for one or the other allele, or heterozygous for both alleles, show no discernible phenotypes. PCR characterization of the long and short alleles shows a poorly defined, artifactual bias toward amplifying the long allele over the short allele. The significance of this polymorphism will be in discerning the largely unknown properties of Nopp140’s large central domain in rDNA transcription and ribosome biogenesis.  more » « less
Award ID(s):
1712975
PAR ID:
10100396
Author(s) / Creator(s):
;
Date Published:
Journal Name:
Molecular Genetics and Genomics
ISSN:
1617-4615
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; (, PLOS Genetics)
    Jaramillo-Lambert, Aimee (Ed.)
    Meiotic recombination plays an important role in ensuring proper chromosome segregation during meiosis I through the creation of chiasmata that connect homologous chromosomes. Recombination plays an additional role in evolution by creating new allelic combinations. Organisms display species-specific crossover patterns, but how these patterns are established is poorly understood.Drosophila mauritianadisplays a different meiotic recombination pattern compared toDrosophila melanogaster, withD. mauritianaexperiencing a reduced centromere effect, the suppression of recombination emanating from the centromeres. To evaluate the contribution of the synaptonemal complex (SC) C(3)G protein to these recombination rate differences, theD. melanogasterallele was replaced withD. mauritiana c(3)Gcoding sequence. We found that theD. mauritianaC(3)G could interact with theD. melanogasterSC machinery to build full length tripartite SC and chromosomes segregated accurately, indicating sufficient crossovers were generated. However, the placement of crossovers was altered, displaying an increase in frequency in the centromere-proximal euchromatin indicating a decrease in the centromere effect, similar to that observed inD. mauritianafemales. Recovery of chromatids with more than one crossover was also increased, likely due to the larger chromosome span now available for crossovers. As replacement of a single gene mediated a strong shift of one species’ crossover pattern towards another species, it indicates a small number of discrete factors may have major influence on species-specific crossover patterning. Additionally, it demonstrates the SC, a structure known to be required for crossover formation in many species, is likely one of these discrete factors. 
    more » « less
  2. ; ; ; ; ; ; ; ; ; ; et al (, microPublication Biology)
    The Drosophila kikkawai feature with NCBI Gene ID 108084518 was determined to be an ortholog of Drosophila melanogaster Sox102F, a member of the FlyBase High Mobility Group Box Transcription Factors gene group (FBgg0000748). Five isoforms were constructed using the GEP F element annotation protocol, the longest being novel isoform Sox102F-PNE (identified using the XM_017180752 RefSeq prediction and RNA-seq data). Among the isoforms found in both D. melanogaster and D. kikkawai, Sox102F-PB is the longest and exhibits a 1.18x coding span expansion due to transposable element insertion into an intron. All D. kikkawai protein isoforms contain the conserved domain HMG_box_dom (IPR009071). 
    more » « less
  3. ; ; ; ; ; ; ; ; ; ; et al (, microPublication biology)
    The Drosophila kikkawai feature with Gene ID 108083276 was determined to be an ortholog of Drosophila melanogaster absent, small, or homeotic discs 1 (ash1). Two isoforms, ash1-PB and ash1-PC, were constructed on the D. kikkawai Muller D element using the GEP annotation protocol. The second coding exon of D. kikkawai ash1 includes an insertion translated into 18 additional amino acids compared to the D. melanogaster protein and is supported by RNA-Seq coverage, the lack of splice junction predictions, and multiple gene predictors. The first intron in both isoforms of D. kikkawai ash1 contains a well conserved non-canonical GC splice site. 
    more » « less
  4. ; ; ; ; ; (, microPublication biology)
    null (Ed.)
    The neprilysin (M13) family of metalloendopeptidases comprises highly conserved ectoenzymes that cleave and thereby inactivate many physiologically relevant peptides in the extracellular space. Impaired neprilysin activity is associated with numerous human diseases. Here, we present a comprehensive list and classification of M13 family members in Drosophila melanogaster. Seven Neprilysin (Nep) genes encode active peptidases, while 21 Neprilysin-like (Nepl) genes encode proteins predicted to be catalytically inactive. RNAseq data demonstrate that all 28 genes are expressed during development, often in a tissue-specific pattern. Most Nep proteins possess a transmembrane domain, whereas almost all Nepl proteins are predicted to be secreted. 
    more » « less
  5. ; ; (, Molecular Ecology)
    Abstract Small RNAs produced from transposable element (TE)‐rich sections of the genome, termed piRNA clusters, are a crucial component in the genomic defence against selfish DNA. In animals, it is thought the invasion of a TE is stopped when a copy of the TE inserts into a piRNA cluster, triggering the production of cognate small RNAs that silence the TE. Despite this importance for TE control, little is known about the evolutionary dynamics of piRNA clusters, mostly because these repeat‐rich regions are difficult to assemble and compare. Here, we establish a framework for studying the evolution of piRNA clusters quantitatively. Previously introduced quality metrics and a newly developed software for multiple alignments of repeat annotations (Manna) allow us to estimate the level of polymorphism segregating in piRNA clusters and the divergence among homologous piRNA clusters. By studying 20 conserved piRNA clusters in multiple assemblies of fourDrosophilaspecies, we show that piRNA clusters are evolving rapidly. While 70%–80% of the clusters are conserved within species, the clusters share almost no similarity between species as closely related asD. melanogasterandD. simulans. Furthermore, abundant insertions and deletions are segregating within theDrosophilaspecies. We show that the evolution of clusters is mainly driven by large insertions of recently active TEs and smaller deletions mostly in older TEs. The effect of these forces is so rapid that homologous clusters often do not contain insertions from the same TE families. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email